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There is increasing molecular and epidemiologic evidence that human papillomavirus (HPV) is associated with a distinct subset of head and neck squamous cell carcinomas. The strength and consistency of HPV DNA presence in oropharyngeal cancers bolster the argument that this association is likely causal. HPV-positive tonsillar cancer in particular is emerging as a specific disease entity with distinct molecular, pathologic, and clinical characteristics. Recent data suggest that the incidence of tonsillar carcinoma in the United States is increasing, despite a decline in tobacco use, supporting the existence of other important risk factors such as HPV infection. Individuals with a history of an HPV-associated anogenital cancer and HIV-infected men are at increased risk for tonsillar carcinoma. This review focuses on the recent literature (since 1998) investigating the relationship between HPV and head and neck cancer development, using the current paradigm for causal inference in epidemiologic research attributed to Sir A. Bradford Hill. Data examining the association of HPV with pathogenesis of head and neck squamous cell carcinoma before 1999 were previously reviewed in this journal.